1) You can create separate scope (Settings | Scopes) that would include those files only. Then, use that scope in separate file watcher .. and in file watcher itself manually reference all files so that all required files will be processed and all output will go into that single file.

2) If that is not possible with YUI Composer (i.e. because it cannot combine multiple files itself -- I have not used it this way myself), then you can create some batch/shell file that would compress all required files first and then merge result files into one. Obviously, you have to use this script instead of actual YUI Compressor in File Watcher.

Double check from what folder that script gets executed (working/current directory). If you do #2 it should definitely help (especially if you edit other .js files in your project). Try setting up correct working directly in your script as well.

For the moment (for debugging purposes) you may set "Show Console" to "Always" so that you can see when file watcher was triggered (close console after sucessfull execution, so you get notified about next launch).

The only thing you may want to do is to pass all required files as a parameters to your script and then loop though them inside (you will have to code this part yourself).

There is one "problem" with this though (possibly it is fixed already, not sure) -- File Watcher passes file names with "/" instead of "\" on Windows as path separators and most of standard Windows/DOS commands do not understand such paths. Therefore you can only pass file names only -- without path (e.g. "myscript.js" instead of "C:\projects\myProject\scripts\myscript.js").

Try deleting the same file again. That's the trick used even in some big popular programs (like Google Chrome). A bit different environment but may work.

Is there any way to get benefit from the file watcher settings like output file name and path

For output file name -- just pass it as FIRST parameter and adjust your code accordingly.

For path -- unlikely (as I have mentioned before -- currently IDE passes path with "/" instead of "\" which Windows/DOS commands do not like. But this needs to be double checked -- possibly it was fixed by now.

also how to use scope

What exactly you want to know?

If you want to use them in this code -- it's not possible. Scope in File Watcher is used to limit the scope (files & folders) on which this particular file watcher will be triggered (in other words: to not to run this File Watcher if you are editing another/unrelated JS file).

P.S.

If you find coding this batch file difficult, maybe it will be easier if you would use another scripting language (e.g. PowerShell/PHP/etc) or even some build tool (like Ant/Phing/Grunt) instead?